BtaINT0130817 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021273 | SEMA4B
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B [Source:HGNC Symbol;Acc:HGNC:10730]
Coordinates
chr21:22036087-22037715:+
Coord C1 exon
chr21:22036087-22036237
Coord A exon
chr21:22036238-22037504
Coord C2 exon
chr21:22037505-22037715
Length
1267 bp
Sequences
Splice sites
5' ss Seq
GCGGTGAGT
5' ss Score
10.49
3' ss Seq
ACCAACGCCTTCTCCTTCAGTGC
3' ss Score
8.5
Exon sequences
Seq C1 exon
GAACGGGGGGACCACGGAGGGCTCTGCCGTCTGTGTCTTCACCATGAAGGACGTGCAGTCCACCTTCAACGGCTTCTACAAGGAGGTGAACCGCGAGACGCAGCAGTGGTACACAGTGACCCACCCAGTACCCTCGCCCCGGCCGGGCGCG
Seq A exon
GTGAGTGCTGCTCCCTGCCGCAGGGCAGCGTGCTGGGAGGACGGGTCCACACCCCGTGCTGGGCTTGCTTGCTTTTTCTAAGCCTGTTGTCTCATCTTGAAAGTGGGGGCAGAACCCAGGGCTGCTTGTCTTTGCAAGTTCGACGTGACCGTGGACATCAGGATGGCAGTGGGCTGGGCAGGGCGGTCCCATCAGAGCGCTGCCTGCAGCATGCCTCTCTCCCACTCCACCGTGAGCTCCTTGTTGAGTGGCTGGCCGTGGGCAAATGGTCCTCTCTTCTTTCCCTCCAGCCTCATGGGCTTCTCACAAAGCAGACCTTGAGACAAGGATATGGGTGCTGGCAGTTTCTAGGGGAGCTACTCCCCGGAAGCAGCAAAGAGGGGACAGGATTGTGGAGGGAGGGGCGGAGCCAAGAAAGCGGGGGTCGCCACACTGCTGCTGCTGTGGGTGCCTGGAGCTGAGGCCCCGGGGCCCTGGGAGGCTATGTGGAGTATATCTCAGCGTCGTCCCACTGGGGTGTTTGTTACCAACTGCTGGGCCTCAGTGATTGAGGGTCACTCTGGGATGTTAATTCTTGGAGCTGCTACAGAGAATGCCCCAGGGCAGAGAGAATCAGGAACCCTTGTGCCGTCACTCAGTCGTGTCCGACTCTTTGTGACCCCATGGACTGTAGCCTGCCAGACTCCTCTGTCCATGGGGATTCTCCAGGCAAGAATACTGGAGTGGGTTGCCATGCCCTCTTCCAGGGGATCTTCCTGACCCAACGACTTGAACTGGGGTCTCCTGCATTGCAGGCGGATTCTTTAACACCTGAGCTATCAGGGAAGCCCAGGAAGCCTCTGGCGATATGGCAGACTAACTGCAGACGCCCTTGTGGCCCCTACACTGGGACACCTTGCTCAGCCAGGGCTTCTTGAGAAAGGAACTCTGTCACTTCCTGCTGAAAGGATGCTACAGGAGCAGAAAGTGCGGTCATGCCCAGGGGAGGGGGTGGGGGAAGGATGGGCAGGAAGGAGAGGTGGTTGGTGGGCAGAGATGGGGAAACCCTGGCAGCCAGGGCCCACGGCCCCACAGCCTTAGACCTGCAGAGAAGCGTGTCGGCTCCACAGAACTGGAGAGCCATGCTGTGGCCTGGCTTCTGAGGGTGGGGGAGTCCCTGCTGTCCACTGGGGAGGCAGGGCGTGGCAATCCCAGCGGGATCTGTAGAACACCCATCCTGCTGGCCACCCCAATGCCGCCCATCTCAAACCAACGCCTTCTCCTTCAG
Seq C2 exon
TGCATCACCAATAGTGCCCGGGAGAGGAAGATCAACTCGTCACTGCAGCTCCCTGACCGCGTGCTGAACTTCCTCAAGGACCACTTCCTGATGGACGGACAGGTCCGCGGCCGCATGTTGCTGCTGCAGCCCCAGGCTCGCTACCAGCATGTGACTGTCCACCGTGTGCTGGCCCTGAACCGCACCTACGACGTCCTCTTCCTGGGCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021273:ENSBTAT00000028346:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.137 A=NA C2=0.056
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(11.4=100)
A:
NA
C2:
PF0140314=Sema=FE(16.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTCTGCCGTCTGTGTCTTC
R:
CAGTGCCCAGGAAGAGGACG
Band lengths:
342-1609
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]